11-118659776-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007180.3(TREH):c.1291G>A(p.Val431Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,583,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007180.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREH | NM_007180.3 | c.1291G>A | p.Val431Met | missense_variant | 11/15 | ENST00000264029.9 | |
TREH | NM_001301065.2 | c.1198G>A | p.Val400Met | missense_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREH | ENST00000264029.9 | c.1291G>A | p.Val431Met | missense_variant | 11/15 | 1 | NM_007180.3 | P1 | |
TREH | ENST00000397925.2 | c.1198G>A | p.Val400Met | missense_variant | 10/14 | 1 | |||
TREH | ENST00000613915.4 | c.*1068G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/13 | 2 | ||||
TREH | ENST00000531295.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000393 AC: 8AN: 203664Hom.: 0 AF XY: 0.0000365 AC XY: 4AN XY: 109616
GnomAD4 exome AF: 0.0000133 AC: 19AN: 1431350Hom.: 0 Cov.: 31 AF XY: 0.00000846 AC XY: 6AN XY: 709136
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1291G>A (p.V431M) alteration is located in exon 11 (coding exon 11) of the TREH gene. This alteration results from a G to A substitution at nucleotide position 1291, causing the valine (V) at amino acid position 431 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at